:
> Message: 3
> Date: Mon, 26 Nov 2012 12:52:48 +
> From: Chris Morley
> Subject: Re: [Open Babel] Tidying up files
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <50b36620.8070...@gaseq.co.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
Chris
My apologies also for the slow response.
OB will already read MDL files with abbreviations in the A (alias) line,
like in the attached file. (But not in the S or R structures.) So
obabel alias2.mol -O expanded2.mol -r
will expand the abbreviations and also remove all disconnected mol
Hi,
Here is a list of abbreviations I have compiled over the years.
Ac, Ace, Acetate, Acetyl, Acyl
AcAc acetoacetyl
ACN = acetonitrile
Ad = 1-adamantyl
Alloc, AOC = allyoxycarbonyl
All, Allyl
Bam = benzamidomethyl
BDMS = biphenyldimethylsilyl
BOC, Boc, t-boc = t-butoxycarbonyl
BOM = benzyloxymet
> I often end up editing files using a text editor because they contain
> features that are not compatible with other programs. In particular removing
> salts and/or solvents and expanding fragment labels e.g TMS, t-butyl etc.
Sorry Chris -- a pile of things stopped me from getting back to this.
Hi,
I often end up editing files using a text editor because they contain features
that are not compatible with other programs. In particular removing salts
and/or solvents and expanding fragment labels e.g TMS, t-butyl etc.
Would it be possible to do this within openbabel, perhaps an "obtidy"
